The current landscape and emerging challenges of benchmarking single-cell methods
- Details
- Publication Year 2025-08-31,Volume 26,Issue #5,Page bbaf380
- Journal Title
- Briefings in Bioinformatics
- Abstract
- With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conducted a systematic literature search and assessed 282 papers, including all 130 benchmark-only papers from the search and an additional 152 method development papers containing benchmarking. This collective effort provides the most comprehensive quantitative summary of the current landscape of single-cell benchmarking studies. We examine performances across nine broad categories, including often ignored aspects such as role of datasets, robustness of methods and downstream evaluation. Our analysis highlights challenges such as how to effectively combine knowledge across multiple benchmarking studies and in what ways can the community recognize the risk and prevent benchmarking fatigue. This paper highlights the importance of adopting a community-led research paradigm to tackle these challenges and establish best practice standards.
- Publisher
- Oxford Academic
- Keywords
- *Single-Cell Analysis/methods/standards; *Benchmarking/methods; Humans; *Computational Biology/methods; benchmarking; single-cell; single-cell method; systematic evaluation
- Research Division(s)
- Bioinformatics and Computational Biology
- PubMed ID
- 41045508
- Publisher's Version
- https://doi.org/10.1093/bib/bbaf380
- Open Access at Publisher's Site
https://doi.org/10.1093/bib/bbaf380- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2025-10-20 01:57:43
Last Modified: 2025-10-20 01:57:58